double cmp[3], p_chi2, lrt; // used by contrast2()
} bcf_p1rst_t;
+typedef struct {
+ double p[4];
+ int mq, depth, is_tested, d[4];
+} anno16_t;
+
#define MC_PTYPE_FULL 1
#define MC_PTYPE_COND2 2
#define MC_PTYPE_FLAT 3
void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_destroy(bcf_p1aux_t *ma);
+ void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+ int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold);
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
void bcf_p1_dump_afs(bcf_p1aux_t *ma);
int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);